Phylogeny of the species-rich pantropical genus Zanthoxylum (Rutaceae) based on hybrid capture

Pantropical regions possess the highest biodiversity on earth yet detailed systematic studies involving pantropical genera often pose significant challenges due to the extensive need for intercontinental sampling. Zanthoxylum, a genus comprising 225 species within the family Rutaceae, provides an excellent model for such studies due to its distribution on most continents and tropical archipelagos. Despite the genus' economic significance, no phylogenetic study with a comprehensive taxon sampling has been conducted. Previous research using Sanger sequencing failed to resolve key questions regarding the genus. To resolve these questions, this study employs the hybrid capture method to: (1) conduct a comprehensive phylogenetic analysis of Zanthoxylum; (2) evaluate Engler's and Reynel's sectional classifications; (3) explore the evolution of the homochlamydeous flower character in section Zanthoxylum; (4) test the monophyly of several species, particularly those with a wide distribution; and (5) to assess hybridization and incomplete lineage sorting in Zanthoxylum. Our analyses resolved Zanthoxylum as monophyletic with four clades centred on different biogeographical regions. Sections Tobinia, Pterota and Zanthoxylum are monophyletic and section Blackburnia and section Macqueria each proved to be polyphyletic. Zanthoxylum s.str. is only monophyletic if Z. clava-herculis and Z. nitidum with heterochlamydeous flowers are placed in it. The separation of Zanthoxylum s.str. into section Sinensis and section Zanthoxylum is not supported. Section Macqueria is highly polyphyletic and spread across three main clades, while section Pterota and section Tobinia are each monophyletic. The widespread Z. asiaticum sampled throughout its distribution from Madagascar and tropical Africa to tropical Asia was found to be monophyletic, representing its own isolated clade within Zanthoxylum. A sectional classification synopsis for Zanthoxylum is provided except that future taxonomic work for section Macqueria is necessary. Quartet sampling suggests incomplete lineage sorting and hybridization within Zanthoxylum.